Skip to content

Commit

Permalink
Update the reverse dependency check results
Browse files Browse the repository at this point in the history
  • Loading branch information
@stefvanbuuren
stefvanbuuren committed Nov 27, 2024
1 parent 8d05b2a commit bb24499
Show file tree
Hide file tree
Showing 3 changed files with 8 additions and 159 deletions.
10 changes: 4 additions & 6 deletions revdep/README.md
View file
Original file line number Diff line number Diff line change
Expand Up @@ -80,11 +80,9 @@
|dynr |0.1.16-105 |1 | | |
|rmsb |1.1-1 |1 | |1 |

## New problems (3)
## New problems (1)

|package |version |error |warning |note |
|:--------|:-------|:------|:-------|:---------|
|[autoReg](problems.md#autoreg)|0.3.3 |__+2__ | | |
|[bipd](problems.md#bipd)|0.3 |1 | |-1 __+1__ |
|[finalfit](problems.md#finalfit)|1.0.8 |__+2__ | |1 |
|package |version |error |warning |note |
|:-------|:-------|:-----|:-------|:---------|
|[bipd](problems.md#bipd)|0.3 |1 | |-1 __+1__ |

12 changes: 2 additions & 10 deletions revdep/cran.md
View file
Original file line number Diff line number Diff line change
Expand Up @@ -2,24 +2,16 @@

We checked 123 reverse dependencies (118 from CRAN + 5 from Bioconductor), comparing R CMD check results across CRAN and dev versions of this package.

* We saw 3 new problems
* We saw 1 new problems
* We failed to check 3 packages

Issues with CRAN packages are summarised below.

### New problems
(This reports the first line of each new failure)

* autoReg
checking examples ... ERROR
checking running R code from vignettes ...

* bipd
checking dependencies in R code ...sh: line 1: 24340 Segmentation fault: 11 R_DEFAULT_PACKAGES=NULL '/Library/Frameworks/R.framework/Resources/bin/R' --vanilla --no-echo 2>&1 < '/var/folders/5_/g85d42yj50b6lrjq4rzjzg8w0000gn/T//RtmpazqvFP/file5c206c170a3d'

* finalfit
checking examples ... ERROR
checking running R code from vignettes ...
checking dependencies in R code ...sh: line 1: 58727 Segmentation fault: 11 R_DEFAULT_PACKAGES=NULL '/Library/Frameworks/R.framework/Resources/bin/R' --vanilla --no-echo 2>&1 < '/var/folders/5_/g85d42yj50b6lrjq4rzjzg8w0000gn/T//RtmpM38C1S/filee1cf761be8f7'

### Failed to check

Expand Down
145 changes: 2 additions & 143 deletions revdep/problems.md
View file
Original file line number Diff line number Diff line change
@@ -1,69 +1,3 @@
# autoReg

<details>

* Version: 0.3.3
* GitHub: https://github.com/cardiomoon/autoReg
* Source code: https://github.com/cran/autoReg
* Date/Publication: 2023-11-14 05:53:27 UTC
* Number of recursive dependencies: 212

Run `revdepcheck::revdep_details(, "autoReg")` for more info

</details>

## Newly broken

* checking examples ... ERROR
```
Running examples in ‘autoReg-Ex.R’ failed
The error most likely occurred in:
> ### Name: autoReg
> ### Title: Perform univariable and multivariable regression and stepwise
> ### backward regression automatically
> ### Aliases: autoReg autoReg.lm autoReg.glm autoReg.coxph autoReg.survreg
>
> ### ** Examples
>
...
9. │ ├─base::withCallingHandlers(...)
10. │ └─dplyr:::mutate_col(dots[[i]], data, mask, new_columns)
11. │ └─mask$eval_all_mutate(quo)
12. │ └─dplyr (local) eval()
13. ├─2.5 %
14. ├─rlang:::`$.rlang_data_pronoun`(.data, `2.5 %`)
15. │ └─rlang:::data_pronoun_get(...)
16. └─rlang:::abort_data_pronoun(x, call = y)
17. └─rlang::abort(msg, "rlang_error_data_pronoun_not_found", call = call)
Execution halted
```
* checking running R code from vignettes ...
```
‘Automatic_Regression_Modeling.Rmd’ using ‘UTF-8’... failed
‘Bootstrap_Prediction.Rmd’ using ‘UTF-8’... OK
‘Getting_started.Rmd’ using ‘UTF-8’... failed
‘Statiastical_test_in_gaze.Rmd’ using ‘UTF-8’... OK
‘Survival.Rmd’ using ‘UTF-8’... OK
ERROR
Errors in running code in vignettes:
when running code in ‘Automatic_Regression_Modeling.Rmd’
...
virginica (N=50) Mean ± SD 6.6 ± 0.6 1.95 (1.75 to 2.14, p<.001) 1.86 (1.65 to 2.07, p<.001)
...
Male 489 (52.9%) 463 (51.6%) 0.95 (0.79-1.14, p=.594) 0.95 (0.78-1.15, p=.589)
——————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————
> autoReg(fit, imputed = TRUE) %>% myft()
When sourcing ‘Getting_started.R’:
Error: ℹ In argument: `lower = exp(.data$`2.5 %`)`.
Caused by error in `` .data$`2.5 %` ``:
! Column `2.5 %` not found in `.data`.
Execution halted
```
# bipd

<details>
Expand All @@ -80,7 +14,7 @@ Run `revdepcheck::revdep_details(, "bipd")` for more info

## Newly broken

* checking dependencies in R code ...sh: line 1: 24340 Segmentation fault: 11 R_DEFAULT_PACKAGES=NULL '/Library/Frameworks/R.framework/Resources/bin/R' --vanilla --no-echo 2>&1 < '/var/folders/5_/g85d42yj50b6lrjq4rzjzg8w0000gn/T//RtmpazqvFP/file5c206c170a3d'
* checking dependencies in R code ...sh: line 1: 58727 Segmentation fault: 11 R_DEFAULT_PACKAGES=NULL '/Library/Frameworks/R.framework/Resources/bin/R' --vanilla --no-echo 2>&1 < '/var/folders/5_/g85d42yj50b6lrjq4rzjzg8w0000gn/T//RtmpM38C1S/filee1cf761be8f7'
```
NOTE
Expand All @@ -107,7 +41,7 @@ Run `revdepcheck::revdep_details(, "bipd")` for more info
## Newly fixed
* checking dependencies in R code ...sh: line 1: 23537 Segmentation fault: 11 R_DEFAULT_PACKAGES=NULL '/Library/Frameworks/R.framework/Resources/bin/R' --vanilla --no-echo 2>&1 < '/var/folders/5_/g85d42yj50b6lrjq4rzjzg8w0000gn/T//RtmpsUM9II/file58f6540265e5'
* checking dependencies in R code ...sh: line 1: 58721 Segmentation fault: 11 R_DEFAULT_PACKAGES=NULL '/Library/Frameworks/R.framework/Resources/bin/R' --vanilla --no-echo 2>&1 < '/var/folders/5_/g85d42yj50b6lrjq4rzjzg8w0000gn/T//Rtmpxl1LPe/filee1b045bcd2d0'
```
NOTE
Expand Down Expand Up @@ -159,78 +93,3 @@ Run `revdepcheck::revdep_details(, "bipd")` for more info
Execution halted
```
# finalfit
<details>
* Version: 1.0.8
* GitHub: https://github.com/ewenharrison/finalfit
* Source code: https://github.com/cran/finalfit
* Date/Publication: 2024-07-24 15:20:01 UTC
* Number of recursive dependencies: 176
Run `revdepcheck::revdep_details(, "finalfit")` for more info
</details>
## Newly broken
* checking examples ... ERROR
```
Running examples in ‘finalfit-Ex.R’ failed
The error most likely occurred in:
> ### Name: missing_predictorMatrix
> ### Title: Create predictorMatrix for use with mice
> ### Aliases: missing_predictorMatrix
>
> ### ** Examples
>
> library(mice)
...
22. │ └─tidyselect:::walk_data_tree(new, data_mask, context_mask)
23. │ └─tidyselect:::as_indices_sel_impl(...)
24. │ └─tidyselect:::as_indices_impl(...)
25. │ └─tidyselect:::chr_as_locations(x, vars, call = call, arg = arg)
26. │ └─vctrs::vec_as_location(...)
27. └─vctrs (local) `<fn>`()
28. └─vctrs:::stop_subscript_oob(...)
29. └─vctrs:::stop_subscript(...)
30. └─rlang::abort(...)
Execution halted
```
* checking running R code from vignettes ...
```
‘all_plots_examples.Rmd’ using ‘UTF-8’... OK
‘all_tables_examples.Rmd’ using ‘UTF-8’... OK
‘bootstrap.Rmd’ using ‘UTF-8’... OK
‘data_prep.Rmd’ using ‘UTF-8’... OK
‘export.Rmd’ using ‘UTF-8’... OK
‘finalfit.Rmd’ using ‘UTF-8’... OK
‘missing.Rmd’ using ‘UTF-8’... failed
‘survival.Rmd’ using ‘UTF-8’... OK
ERROR
Errors in running code in vignettes:
...
> fits_pool = fits %>% pool()
> colon_s %>% or_plot(dependent, explanatory, glmfit = fits_pool,
+ table_text_size = 4)
Note: dependent includes missing data. These are dropped.
When sourcing ‘missing.R’:
Error: Can't select columns that don't exist.
✖ Column `2.5 %` doesn't exist.
Execution halted
```
## In both
* checking installed package size ... NOTE
```
installed size is 5.6Mb
sub-directories of 1Mb or more:
doc 4.9Mb
```

0 comments on commit bb24499

Please sign in to comment.